IDF1 patch panel should lead to patch panels in another switch closet and the same with IDF2. You would not connect these two panels to each other. You would need to determine if devices were attached at the other end in the IDF’s. Then connect the appropriate pairs to fiber interfaces on the switch or convert from fiber to copper and connect into standard RJ45 switch ports. In other words, there should be another LAN switch in IDF1 with fiber connections to ports 1/2 which then connect in the MDF to a GBIC on the main switch.
Do you have any connection between the Linksys switch and the WAN router? You need to have a path from the LAN to the internet. You cannot connect the LAN switch to the T1 jack from AT&T. The T1 link should go to a router. It sounds like you need to work with a local network consultant for a quick effort on getting this all configured and properly secured. There is a lot of troubleshooting here that would be much easier with hands-on and eyes-on local support. We will be glad to help, but this may be a bit more difficult if you have never built a LAN/WAN with these types of interconnections. We all started somewhere, and it is usually best to have a local partner to work with and get some on-the-job-training for something like this.
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